Title: Random Network Model Selection and Parameter Tuning
Description: Model selection and parameter tuning procedures for a class of random network models. The model selection can be done by a general cross-validation framework called ECV from Li et. al. (2016) <arXiv:1612.04717> . Several other model-based and task-specific methods are also included, such as NCV from Chen and Lei (2016) <arXiv:1411.1715>, likelihood ratio method from Wang and Bickel (2015) <arXiv:1502.02069>, spectral methods from Le and Levina (2015) <arXiv:1507.00827>. Many network analysis methods are also implemented, such as the regularized spectral clustering (Amini et. al. 2013 <doi:10.1214/13-AOS1138>) and its degree corrected version and graphon neighborhood smoothing (Zhang et. al. 2015 <arXiv:1509.08588>).
Author: Tianxi Li, Elizaveta Levina, Ji Zhu
Maintainer: Tianxi Li <tianxili@umich.edu>
Diff between randnet versions 0.1 dated 2017-09-17 and 0.2 dated 2019-02-12
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 +- R/RCode.R | 48 ++++++++++++++++++++++++++++++++++++++++++++---- man/ConcensusClust.Rd |only man/LRBIC.Rd | 3 ++- man/NCV.select.Rd | 4 ++-- man/nSmooth.Rd | 4 +++- man/randnet-package.Rd | 49 ++++++++++++++++++++++++++++++++++++++++++++++--- 9 files changed, 110 insertions(+), 23 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A convenient interface for making
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Stephen Hoover [ctb],
Danning Chen [ctb],
Elizabeth Sander [ctb],
Madison Hobbs [ctb],
Anna Bladey [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.5.1 dated 2018-08-15 and 1.6.1 dated 2019-02-12
DESCRIPTION | 16 MD5 | 38 +- NAMESPACE | 2 R/civis_ml_utils.R | 45 ++ R/generate_client.R | 2 R/io.R | 112 +++--- build/vignette.rds |binary inst/doc/civis_ml.Rmd | 2 inst/doc/civis_ml.html | 510 ++++++++++++++++++++-------- inst/doc/concurrency.html | 460 ++++++++++++++++++------- inst/doc/data_import_and_export.html | 392 +++++++++++++++++---- inst/doc/quick_start.html | 416 +++++++++++++++++----- man/coef.civis_ml.Rd |only man/get_feature_importance.Rd |only man/write_civis.Rd | 26 + tests/testthat/data/feature_importances.rds |only tests/testthat/data/model_coefficients.rds |only tests/testthat/test_autogen.R | 2 tests/testthat/test_civis_ml_utils.R | 29 + tests/testthat/test_io.R | 74 +++- tools/integration_tests/smoke_test.R | 6 vignettes/civis_ml.Rmd | 2 22 files changed, 1616 insertions(+), 518 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.12 dated 2018-10-09 and 0.13 dated 2019-02-12
DESCRIPTION | 8 ++++---- MD5 | 41 +++++++++++++++++++++-------------------- NEWS | 7 +++++++ R/eval.r | 39 ++++++++++++++++++++++----------------- R/hooks.r | 4 ++-- R/output.r | 18 +++++++++--------- R/parse.r | 11 ++++++----- R/replay.r | 8 ++++---- R/traceback.r | 4 ++-- R/watcher.r | 17 +++++++++-------- man/create_traceback.Rd | 2 +- man/evaluate.Rd | 8 ++++---- man/flush_console.Rd | 4 ++-- man/inject_funs.Rd | 2 +- man/new_output_handler.Rd | 10 +++++----- man/parse_all.Rd | 8 ++++---- man/replay.Rd | 2 +- man/set_hooks.Rd | 2 +- man/try_capture_stack.Rd | 2 +- man/watchout.Rd | 2 +- tests/testthat/test-errors.r | 7 +++++++ tests/testthat/try.r |only 22 files changed, 114 insertions(+), 92 deletions(-)
Title: Collection of Scripts for Interface Between 'Cornerstone' and
'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'.
---
The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>)
is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster.
The engineers incorporate intensified hands-on statistics into their projects.
They benefit from an intuitive and uniquely designed graphical Workmap concept: you design
experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon,
immediately, interactively, and without any programming.
---
While 'Cornerstone's' interface to the statistical programming language 'R' has been available
since version 6.0, the latest interface with 'R' is even much more efficient.
'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the
standard 'Cornerstone' GUI.
Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R'
routines, immediately and without the need to deal with programming code.
---
Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel
(<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>
Diff between CornerstoneR versions 1.1.0 dated 2019-02-12 and 1.1.1 dated 2019-02-12
CornerstoneR-1.1.0/CornerstoneR/tests/testthat/Rplots.pdf |only CornerstoneR-1.1.1/CornerstoneR/DESCRIPTION | 12 ++++++------ CornerstoneR-1.1.1/CornerstoneR/MD5 | 7 +++---- CornerstoneR-1.1.1/CornerstoneR/NEWS.md | 3 +++ CornerstoneR-1.1.1/CornerstoneR/man/CornerstoneR-package.Rd | 6 +++--- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Simulate Genotypes from the BN-PSD Admixture Model
Description: The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre],
John D. Storey [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between bnpsd versions 1.0.1 dated 2018-01-16 and 1.0.4 dated 2019-02-12
DESCRIPTION | 12 +++--- MD5 | 30 ++++++++------- NAMESPACE | 2 + NEWS.md | 19 +++++++++ R/coanc_to_kinship.R |only R/fixed_loci.R |only R/rbnpsd.R | 20 +++++++++- build/vignette.rds |binary inst/doc/bnpsd.Rmd | 7 +-- inst/doc/bnpsd.pdf |binary man/bnpsd.Rd | 2 - man/coanc_to_kinship.Rd |only man/fixed_loci.Rd |only man/q1d.Rd | 4 +- man/q1dc.Rd | 4 +- man/rbnpsd.Rd | 6 ++- tests/testthat/test_bnpsd.R | 85 ++++++++++++++++++++++++++++++++++++++++++++ vignettes/bnpsd.Rmd | 7 +-- 18 files changed, 163 insertions(+), 35 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch>, Sören Vogel <soeren.vogel@posteo.ch>, Oliver Jakoby <oliver.jakoby@rifcon.de> and Alexander Singer <alexander.singer@rifcon.de>
Maintainer: Oliver Jakoby <oliver.jakoby@rifcon.de>
Diff between GUTS versions 1.0.4 dated 2017-10-10 and 1.1.0 dated 2019-02-12
DESCRIPTION | 21 - MD5 | 36 +- NAMESPACE | 26 + R/GUTS.R | 696 ++++++++++++++++++++++++++-------------------------- R/RcppExports.R |only build |only data/diazinon.rda |binary inst |only man/GUTS-package.Rd | 82 +++--- man/GUTS.Rd | 449 +++++++++++++++++++-------------- man/diazinon.Rd | 28 +- src/RcppExports.cpp | 22 - src/guts_engine.cpp | 562 +++++++++++++++++++++++------------------ src/init.c | 5 vignettes |only 15 files changed, 1050 insertions(+), 877 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-31 0.1.0
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.6-0 dated 2017-10-29 and 1.7-0 dated 2019-02-12
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ R/griddev.R | 63 +++++++++++++++++++++++++++++++++++---------- R/svgStrings.R | 9 +++--- build/vignette.rds |binary inst/NEWS.Rd | 13 ++++++++- inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary tests/testsvg.R | 8 ++--- 10 files changed, 83 insertions(+), 36 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 6.3.0 dated 2018-11-21 and 7.0.0 dated 2019-02-12
Delaporte-6.3.0/Delaporte/tests/testthat/test-delap.r |only Delaporte-7.0.0/Delaporte/DESCRIPTION | 9 + Delaporte-7.0.0/Delaporte/MD5 | 26 +++-- Delaporte-7.0.0/Delaporte/README.md | 10 +- Delaporte-7.0.0/Delaporte/build/partial.rdb |binary Delaporte-7.0.0/Delaporte/inst/NEWS.Rd | 23 ++++- Delaporte-7.0.0/Delaporte/man/Delaporte-package.Rd | 4 Delaporte-7.0.0/Delaporte/man/Delaporte.Rd | 16 +-- Delaporte-7.0.0/Delaporte/src/Makevars | 22 +--- Delaporte-7.0.0/Delaporte/src/delaporte.f95 | 69 +++++++-------- Delaporte-7.0.0/Delaporte/src/utils.f95 | 23 ----- Delaporte-7.0.0/Delaporte/src/utils_and_wrappers.c | 2 Delaporte-7.0.0/Delaporte/tests/testthat/test-ddelap.r |only Delaporte-7.0.0/Delaporte/tests/testthat/test-momdelap.r |only Delaporte-7.0.0/Delaporte/tests/testthat/test-pdelap.r |only Delaporte-7.0.0/Delaporte/tests/testthat/test-qdelap.r |only Delaporte-7.0.0/Delaporte/tests/testthat/test-rdelap.r |only 17 files changed, 106 insertions(+), 98 deletions(-)
Title: Quantitative Analysis Made Accessible
Description: This is a new version of the 'userfriendlyscience' package,
which has grown a bit unwieldy. Therefore, distinct functionalities
are being 'consciously uncoupled' into different packages. This package
contains the general-purpose tools and utilities (see the
'behaviorchange' and the 'rosetta' packages for other functionality), and
is the most direct 'successor' of the original 'userfriendlyscience' package.
For example, this package contains a number of basic functions to create
higher level plots, such as diamond plots, to easily plot sampling
distributions, to generate confidence intervals, to plan study sample sizes
for confidence intervals, and to do some basic operations such as
(dis)attenuate effect size estimates.
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between ufs versions 0.1.0 dated 2019-01-16 and 0.2.0 dated 2019-02-12
DESCRIPTION | 10 +- MD5 | 158 ++++++++++++++++---------------- NAMESPACE | 7 + R/areColors.R | 2 R/associationMatrix.R | 48 +++++---- R/associationsDiamondPlot.R | 28 ++--- R/attenuate.d.R | 2 R/attenuate.r.R |only R/biAxisDiamondPlot.R | 26 ++--- R/cohensdCI.R | 64 +++++++++--- R/cohensdDist.R | 128 +++++++++++++------------ R/confIntOmegaSq.R | 8 - R/confIntProp.R | 14 +- R/confIntR.R | 12 +- R/convert.R | 23 ++-- R/convert.d.to.nnc.R | 2 R/crossTab.R |only R/diamondPlot.R | 22 ++-- R/disattenuate.r.R |only R/duoComparisonDiamondPlot.R | 2 R/faConfInt.R | 10 +- R/factorLoadingDiamondCIplot.R | 22 ++-- R/formatCI.R | 2 R/formatPvalue.R | 4 R/formatR.R | 2 R/from_MBESS_conf.limits.nct.R |only R/getData.R | 14 +- R/ggDiamondLayer.R | 54 +++++----- R/ggEasyBar.R | 18 +-- R/ggProportionPlot.R | 16 +-- R/is.nr.R | 2 R/meanSDtoDiamondPlot.R | 14 +- R/meansComparisonDiamondPlot.R | 40 ++++---- R/meansDiamondPlot.R | 24 ++-- R/multiResponse.R | 12 +- R/multiVarFreq.R | 16 ++- R/noZero.R | 2 R/omegaSqDist.R | 24 ++-- R/pwr.cohensdCI.R | 52 ++++++++-- R/repeatStr.R |only man/areColors.Rd | 2 man/associationMatrix.Rd | 19 +++ man/associationMatrixHelperFunctions.Rd | 14 +- man/associationsDiamondPlot.Rd | 10 +- man/attenuate.d.Rd | 4 man/attenuate.r.Rd |only man/basicDiamondplotFunctions.Rd | 30 +++--- man/biAxisDiamondPlot.Rd | 18 +-- man/cat0.Rd | 6 - man/cohensDdistribution.Rd | 27 +++-- man/comparisonDiamondPlots.Rd | 17 +-- man/confIntOmegaSq.Rd | 10 +- man/confIntProp.Rd | 14 +- man/confIntR.Rd | 8 - man/convert.Rd | 2 man/convert.d.to.nnc.Rd | 8 - man/convertToNumeric.Rd | 2 man/cramersV.Rd | 2 man/diamondPlot.Rd | 18 +-- man/disattenuate.r.Rd |only man/extractVarName.Rd | 2 man/faConfInt.Rd | 12 +- man/factorLoadingDiamondCIplot.Rd | 28 ++--- man/formatCI.Rd | 4 man/formatPvalue.Rd | 10 +- man/formatR.Rd | 2 man/getData.Rd | 2 man/ggBarChart.Rd | 10 +- man/ggEasyPlots.Rd | 13 +- man/ggProportionPlot.Rd | 18 +-- man/ifelseObj.Rd | 2 man/isTrue.Rd | 8 - man/makeScales.Rd | 4 man/massConvertToNumeric.Rd | 6 - man/meanConfInt.Rd | 8 - man/meanSDtoDiamondPlot.Rd | 12 +- man/meansDiamondPlot.Rd | 19 +-- man/multiResponse.Rd | 2 man/multiVarFreq.Rd | 4 man/noZero.Rd | 2 man/omegasq.Rd | 14 +- man/repeatStr.Rd |only man/sharedSubString.Rd | 2 man/vecTxt.Rd | 16 +-- 84 files changed, 709 insertions(+), 586 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-03 0.1.0
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on
'htmlwidgets', it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced but
can easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at <http://datastorm-
open.github.io/introduction_ramcharts/> and <http://www.amcharts.com/> for
more information about the library. The package includes the free version
of 'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate to refer
to this page <http://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Benoit Thieurmel [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Jeffery Petit [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between rAmCharts versions 2.1.9 dated 2018-11-05 and 2.1.10 dated 2019-02-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/chart_amBoxplot.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: A Friendly Package Manager
Description: Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Diff between jetpack versions 0.4.1 dated 2018-11-16 and 0.4.2 dated 2019-02-12
jetpack-0.4.1/jetpack/R/jetpack.R |only jetpack-0.4.2/jetpack/DESCRIPTION | 8 +-- jetpack-0.4.2/jetpack/MD5 | 41 ++++++++++++-------- jetpack-0.4.2/jetpack/NAMESPACE | 3 - jetpack-0.4.2/jetpack/NEWS.md | 5 ++ jetpack-0.4.2/jetpack/R/add.R |only jetpack-0.4.2/jetpack/R/check.R |only jetpack-0.4.2/jetpack/R/cli.R |only jetpack-0.4.2/jetpack/R/global.R |only jetpack-0.4.2/jetpack/R/helpers.R |only jetpack-0.4.2/jetpack/R/init.R |only jetpack-0.4.2/jetpack/R/install.R |only jetpack-0.4.2/jetpack/R/load.R |only jetpack-0.4.2/jetpack/R/outdated.R |only jetpack-0.4.2/jetpack/R/remove.R |only jetpack-0.4.2/jetpack/R/run.R |only jetpack-0.4.2/jetpack/R/update.R |only jetpack-0.4.2/jetpack/man/add.Rd | 2 jetpack-0.4.2/jetpack/man/check.Rd | 2 jetpack-0.4.2/jetpack/man/cli.Rd | 2 jetpack-0.4.2/jetpack/man/init.Rd | 2 jetpack-0.4.2/jetpack/man/install.Rd | 2 jetpack-0.4.2/jetpack/man/load.Rd | 2 jetpack-0.4.2/jetpack/man/outdated.Rd | 2 jetpack-0.4.2/jetpack/man/remove.Rd | 2 jetpack-0.4.2/jetpack/man/run.Rd | 2 jetpack-0.4.2/jetpack/man/update.Rd | 2 jetpack-0.4.2/jetpack/tests/testthat/test-jetpack.R | 2 28 files changed, 46 insertions(+), 33 deletions(-)
Title: Collection of Scripts for Interface Between 'Cornerstone' and
'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'.
\cr\cr
The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>)
is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster.
The engineers incorporate intensified hands-on statistics into their projects.
They benefit from an intuitive and uniquely designed graphical Workmap concept: you design
experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon,
immediately, interactively, and without any programming.
\cr\cr
While 'Cornerstone's' interface to the statistical programming language 'R' has been available
since version 6.0, the latest interface with 'R' is even much more efficient.
'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the
standard 'Cornerstone' GUI.
Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R'
routines, immediately and without the need to deal with programming code.
\cr\cr
Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel
(<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>
Diff between CornerstoneR versions 1.0.1 dated 2018-12-18 and 1.1.0 dated 2019-02-12
CornerstoneR-1.0.1/CornerstoneR/inst/tobedone |only CornerstoneR-1.1.0/CornerstoneR/DESCRIPTION | 35 + CornerstoneR-1.1.0/CornerstoneR/MD5 | 57 +-- CornerstoneR-1.1.0/CornerstoneR/NAMESPACE | 1 CornerstoneR-1.1.0/CornerstoneR/NEWS.md | 7 CornerstoneR-1.1.0/CornerstoneR/R/fitFunction.R | 110 ++++- CornerstoneR-1.1.0/CornerstoneR/R/helper.R | 23 + CornerstoneR-1.1.0/CornerstoneR/R/localInterface.R | 24 + CornerstoneR-1.1.0/CornerstoneR/R/mosaicPlot.R | 11 CornerstoneR-1.1.0/CornerstoneR/R/randomForest.R | 82 ++-- CornerstoneR-1.1.0/CornerstoneR/R/randomForestPredict.R |only CornerstoneR-1.1.0/CornerstoneR/R/reshapeLong.R | 6 CornerstoneR-1.1.0/CornerstoneR/R/reshapeWide.R | 6 CornerstoneR-1.1.0/CornerstoneR/R/zzz.R | 2 CornerstoneR-1.1.0/CornerstoneR/README.md | 28 + CornerstoneR-1.1.0/CornerstoneR/inst/csdata/functionList.txt | 7 CornerstoneR-1.1.0/CornerstoneR/inst/variablesdialog/fitFunction.xml | 7 CornerstoneR-1.1.0/CornerstoneR/inst/variablesdialog/randomForest.xml | 2 CornerstoneR-1.1.0/CornerstoneR/man/CornerstoneR-package.Rd |only CornerstoneR-1.1.0/CornerstoneR/man/LocalInterface.Rd | 17 CornerstoneR-1.1.0/CornerstoneR/man/fitFunction.Rd | 49 ++ CornerstoneR-1.1.0/CornerstoneR/man/mosaicPlot.Rd | 11 CornerstoneR-1.1.0/CornerstoneR/man/randomForest.Rd | 42 +- CornerstoneR-1.1.0/CornerstoneR/man/randomForestPredict.Rd |only CornerstoneR-1.1.0/CornerstoneR/man/reshapeLong.Rd | 14 CornerstoneR-1.1.0/CornerstoneR/man/reshapeWide.Rd | 16 CornerstoneR-1.1.0/CornerstoneR/tests/testthat/Rplots.pdf |binary CornerstoneR-1.1.0/CornerstoneR/tests/testthat/test_fitFunction.R | 169 +++++++- CornerstoneR-1.1.0/CornerstoneR/tests/testthat/test_functionList.R | 2 CornerstoneR-1.1.0/CornerstoneR/tests/testthat/test_randomForest.R | 189 ++++++++-- CornerstoneR-1.1.0/CornerstoneR/tests/testthat/test_reshape.R | 1 31 files changed, 716 insertions(+), 202 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA). Data is obtained from Protected Planet
<http://protectedplanet.net>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 0.0.1 dated 2019-01-11 and 0.0.2 dated 2019-02-12
DESCRIPTION | 15 ++++----- MD5 | 29 +++++++++-------- NEWS.md |only R/geo.R | 3 + R/internal.R | 6 +++ R/wdpa_clean.R | 18 +++++++--- R/wdpa_url.R | 1 README.md | 31 +++++++++--------- build/vignette.rds |binary inst/CITATION | 11 +++++- inst/doc/wdpar.html | 60 +++++++++++++++++------------------- man/figures/README-readme-map-1.png |binary man/wdpa_clean.Rd | 2 - tests/testthat/test_internal.R | 4 ++ tests/testthat/test_wdpa_clean.R | 34 ++++++++++++++++++-- tests/testthat/test_wdpa_fetch.R | 4 +- 16 files changed, 136 insertions(+), 82 deletions(-)
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
R package for matching 'HTTP' requests by various rules ('HTTP' method,
'URL', query parameters, headers, body, etc.), and then caching
real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
matching any previous requests in the same 'cassette' use a cached
'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between vcr versions 0.2.2 dated 2019-01-13 and 0.2.6 dated 2019-02-12
DESCRIPTION | 23 ++-- MD5 | 74 +++++++------- NAMESPACE | 1 NEWS.md | 21 ++++ R/cassette_class.R | 81 ++++++++++----- R/cassettes.R | 18 +-- R/configuration.R | 2 R/errors.R | 20 ++- R/onLoad.R | 4 R/real_connections.R | 5 R/recording.R | 2 R/request_handler-crul.R | 3 R/request_handler-httr.R | 15 +- R/request_handler.R | 24 ++++ R/response_class.R | 33 +++--- R/serialize_to_crul.R | 4 R/serialize_to_httr.R | 3 R/use_cassette.R | 33 +++++- R/vcr_setup.R |only R/write.R | 1 R/zzz.R | 10 + README.md | 27 ++++- inst/doc/configuration.html | 4 inst/doc/request_matching.html | 4 inst/doc/vcr_vignette.html | 4 man/RequestHandler.Rd | 19 +++ man/recording.Rd | 2 man/use_cassette.Rd | 33 +++++- man/use_vcr.Rd |only tests/testthat/helper-vcr.R | 22 ++++ tests/testthat/httr_obj.rda |only tests/testthat/test-Cassette.R | 4 tests/testthat/test-Persisters.R | 4 tests/testthat/test-ause_cassette.R | 12 +- tests/testthat/test-ause_cassette_record_modes.R |only tests/testthat/test-cassettes.R | 8 - tests/testthat/test-eject_cassette.R | 10 - tests/testthat/test-errors.R | 118 ++++++++++++++++++++++- tests/testthat/test-httr.R |only tests/testthat/test-insert_cassette.R | 8 - tests/testthat/test-use_vcr.R |only 41 files changed, 486 insertions(+), 170 deletions(-)
Title: Extension for 'R6' Base Class
Description: Useful methods and data fields to extend the
bare bones 'R6' class provided by the 'R6' package - ls-method,
hashes, warning- and message-method, general get-method and a
debug-method that assigns self and private to the global environment.
Author: Peter Meissner [aut, cre]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between r6extended versions 0.1.1 dated 2018-01-15 and 0.1.2 dated 2019-02-12
DESCRIPTION | 10 - LICENSE | 4 MD5 | 16 +- NAMESPACE | 14 +- NEWS.md | 8 + README.md | 374 +++++++++++++++++++++++++++--------------------------- man/pipe.Rd | 18 +- man/r6e_hash.Rd | 30 ++-- man/r6extended.Rd | 94 ++++++------- 9 files changed, 294 insertions(+), 274 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in
photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse
ratios and other derived quantities from spectral data. Local maxima and
minima. Conversion between energy- and photon-based units. Wavelength
interpolation. Astronomical calculations related solar angles and day
length. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.9.25 dated 2018-12-11 and 0.9.26 dated 2019-02-12
photobiology-0.9.25/photobiology/man/c.generic_mspct.Rd |only photobiology-0.9.25/photobiology/man/na.omit.source_spct.Rd |only photobiology-0.9.26/photobiology/DESCRIPTION | 20 photobiology-0.9.26/photobiology/MD5 | 187 - photobiology-0.9.26/photobiology/NAMESPACE | 77 photobiology-0.9.26/photobiology/NEWS | 21 photobiology-0.9.26/photobiology/R/copy.attr.R | 16 photobiology-0.9.26/photobiology/R/head-tail.R | 14 photobiology-0.9.26/photobiology/R/insert.hinges.r | 38 photobiology-0.9.26/photobiology/R/mspct.mean.r |only photobiology-0.9.26/photobiology/R/mspct.mean.se.r |only photobiology-0.9.26/photobiology/R/mspct.median.r |only photobiology-0.9.26/photobiology/R/mspct.prod.r |only photobiology-0.9.26/photobiology/R/mspct.range.r |only photobiology-0.9.26/photobiology/R/mspct.row.funs.r |only photobiology-0.9.26/photobiology/R/mspct.sd.r |only photobiology-0.9.26/photobiology/R/mspct.se.r |only photobiology-0.9.26/photobiology/R/mspct.sum.r |only photobiology-0.9.26/photobiology/R/mspct.var.r |only photobiology-0.9.26/photobiology/R/na.rm.R | 303 +- photobiology-0.9.26/photobiology/R/photobiology.r | 1 photobiology-0.9.26/photobiology/R/rbindspct.r | 70 photobiology-0.9.26/photobiology/R/spct.conversion.R | 5 photobiology-0.9.26/photobiology/R/spct.insert.spct.hinges.r | 60 photobiology-0.9.26/photobiology/R/spct.smooth.spct.r | 179 - photobiology-0.9.26/photobiology/R/sun.calc.r | 2 photobiology-0.9.26/photobiology/R/water.vapour.R | 295 +- photobiology-0.9.26/photobiology/build/vignette.rds |binary photobiology-0.9.26/photobiology/data/A.illuminant.spct.rda |binary photobiology-0.9.26/photobiology/data/D2-FEL-constants.rda |binary photobiology-0.9.26/photobiology/data/D65.illuminant.spct.rda |binary photobiology-0.9.26/photobiology/data/Ler-leaf-spct.rda |binary photobiology-0.9.26/photobiology/data/beesxyz.spct.rda |binary photobiology-0.9.26/photobiology/data/black_body.spct.rda |binary photobiology-0.9.26/photobiology/data/ccd.spct.rda |binary photobiology-0.9.26/photobiology/data/ciev10.spct.rda |binary photobiology-0.9.26/photobiology/data/ciev2.spct.rda |binary photobiology-0.9.26/photobiology/data/ciexyzCC10.spct.rda |binary photobiology-0.9.26/photobiology/data/ciexyzCC2.spct.rda |binary photobiology-0.9.26/photobiology/data/ciexyzCMF10.spct.rda |binary photobiology-0.9.26/photobiology/data/ciexyzCMF2.spct.rda |binary photobiology-0.9.26/photobiology/data/clear.spct.rda |binary photobiology-0.9.26/photobiology/data/clear_body.spct.rda |binary photobiology-0.9.26/photobiology/data/filter-cps-mspct.rda |binary photobiology-0.9.26/photobiology/data/green_leaf.spct.rda |binary photobiology-0.9.26/photobiology/data/opaque.spct.rda |binary photobiology-0.9.26/photobiology/data/photodiode.spct.rda |binary photobiology-0.9.26/photobiology/data/polyester.spct.rda |binary photobiology-0.9.26/photobiology/data/sun.daily.data.rda |binary photobiology-0.9.26/photobiology/data/sun.daily.spct.rda |binary photobiology-0.9.26/photobiology/data/sun.data.rda |binary photobiology-0.9.26/photobiology/data/sun.spct.rda |binary photobiology-0.9.26/photobiology/data/white-led-spct.rda |binary photobiology-0.9.26/photobiology/data/white_body.spct.rda |binary photobiology-0.9.26/photobiology/data/yellow.gel.rda |binary photobiology-0.9.26/photobiology/inst/doc/userguide1-intro.html | 198 - photobiology-0.9.26/photobiology/inst/doc/userguide2-radiation.R | 15 photobiology-0.9.26/photobiology/inst/doc/userguide2-radiation.Rmd | 70 photobiology-0.9.26/photobiology/inst/doc/userguide2-radiation.html | 1328 +++++----- photobiology-0.9.26/photobiology/inst/doc/userguide3-astronomy.R | 15 photobiology-0.9.26/photobiology/inst/doc/userguide3-astronomy.Rmd | 51 photobiology-0.9.26/photobiology/inst/doc/userguide3-astronomy.html | 542 +--- photobiology-0.9.26/photobiology/man/as_energy.Rd | 3 photobiology-0.9.26/photobiology/man/as_quantum_mol.Rd | 3 photobiology-0.9.26/photobiology/man/c.Rd |only photobiology-0.9.26/photobiology/man/calc_multipliers.Rd | 3 photobiology-0.9.26/photobiology/man/copy_attributes.Rd | 11 photobiology-0.9.26/photobiology/man/div_spectra.Rd | 3 photobiology-0.9.26/photobiology/man/energy_irradiance.Rd | 3 photobiology-0.9.26/photobiology/man/energy_ratio.Rd | 3 photobiology-0.9.26/photobiology/man/extract.Rd | 7 photobiology-0.9.26/photobiology/man/head_tail.Rd | 14 photobiology-0.9.26/photobiology/man/insert_hinges.Rd | 3 photobiology-0.9.26/photobiology/man/integrate_xy.Rd | 3 photobiology-0.9.26/photobiology/man/interpolate_spectrum.Rd | 3 photobiology-0.9.26/photobiology/man/irradiance.Rd | 3 photobiology-0.9.26/photobiology/man/l_insert_hinges.Rd | 3 photobiology-0.9.26/photobiology/man/na.omit.Rd |only photobiology-0.9.26/photobiology/man/oper_spectra.Rd | 3 photobiology-0.9.26/photobiology/man/photon_irradiance.Rd | 3 photobiology-0.9.26/photobiology/man/photon_ratio.Rd | 3 photobiology-0.9.26/photobiology/man/photons_energy_ratio.Rd | 3 photobiology-0.9.26/photobiology/man/prod_spectra.Rd | 3 photobiology-0.9.26/photobiology/man/rowwise.Rd |only photobiology-0.9.26/photobiology/man/s_e_irrad2rgb.Rd | 3 photobiology-0.9.26/photobiology/man/s_mean.Rd |only photobiology-0.9.26/photobiology/man/s_mean_se.Rd |only photobiology-0.9.26/photobiology/man/s_median.Rd |only photobiology-0.9.26/photobiology/man/s_prod.Rd |only photobiology-0.9.26/photobiology/man/s_range.Rd |only photobiology-0.9.26/photobiology/man/s_sd.Rd |only photobiology-0.9.26/photobiology/man/s_se.Rd |only photobiology-0.9.26/photobiology/man/s_sum.Rd |only photobiology-0.9.26/photobiology/man/s_var.Rd |only photobiology-0.9.26/photobiology/man/se.Rd |only photobiology-0.9.26/photobiology/man/smooth_spct.Rd | 18 photobiology-0.9.26/photobiology/man/split_energy_irradiance.Rd | 3 photobiology-0.9.26/photobiology/man/split_photon_irradiance.Rd | 3 photobiology-0.9.26/photobiology/man/subset.Rd |only photobiology-0.9.26/photobiology/man/subt_spectra.Rd | 3 photobiology-0.9.26/photobiology/man/sum_spectra.Rd | 3 photobiology-0.9.26/photobiology/man/sun_angles.Rd | 2 photobiology-0.9.26/photobiology/man/trim_tails.Rd | 3 photobiology-0.9.26/photobiology/man/v_insert_hinges.Rd | 4 photobiology-0.9.26/photobiology/man/v_replace_hinges.Rd |only photobiology-0.9.26/photobiology/man/water_vp_sat.Rd | 163 - photobiology-0.9.26/photobiology/vignettes/userguide2-radiation.Rmd | 70 photobiology-0.9.26/photobiology/vignettes/userguide3-astronomy.Rmd | 51 108 files changed, 2322 insertions(+), 1591 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2019) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.6.4 dated 2018-11-25 and 1.6.5 dated 2019-02-12
lava-1.6.4/lava/R/org.R |only lava-1.6.4/lava/man/Org.Rd |only lava-1.6.5/lava/DESCRIPTION | 16 +++--- lava-1.6.5/lava/MD5 | 56 +++++++++++------------ lava-1.6.5/lava/NAMESPACE | 1 lava-1.6.5/lava/NEWS | 4 + lava-1.6.5/lava/R/binomial.rrw.R | 23 ++++++++- lava-1.6.5/lava/R/estimate.default.R | 2 lava-1.6.5/lava/R/gkgamma.R | 2 lava-1.6.5/lava/R/logLik.R | 2 lava-1.6.5/lava/R/parlabels.R | 2 lava-1.6.5/lava/R/plot.estimate.R | 2 lava-1.6.5/lava/R/print.R | 8 ++- lava-1.6.5/lava/R/sim.lvm.R | 6 -- lava-1.6.5/lava/data/bmd.rda |binary lava-1.6.5/lava/data/bmidata.rda |binary lava-1.6.5/lava/data/brisa.rda |binary lava-1.6.5/lava/data/calcium.rda |binary lava-1.6.5/lava/data/hubble.rda |binary lava-1.6.5/lava/data/hubble2.rda |binary lava-1.6.5/lava/data/indoorenv.rda |binary lava-1.6.5/lava/data/missingdata.rda |binary lava-1.6.5/lava/data/nldata.rda |binary lava-1.6.5/lava/data/nsem.rda |binary lava-1.6.5/lava/data/semdata.rda |binary lava-1.6.5/lava/data/serotonin.rda |binary lava-1.6.5/lava/data/serotonin2.rda |binary lava-1.6.5/lava/data/twindata.rda |binary lava-1.6.5/lava/inst/CITATION | 78 ++++++++++++++++++++++----------- lava-1.6.5/lava/inst/doc/reference.pdf |binary 30 files changed, 125 insertions(+), 77 deletions(-)
Title: Access the 'languagelayer' API
Description: Improve your text analysis with languagelayer
<https://languagelayer.com>, a powerful language detection
API.
Author: Colin FAY [aut, cre]
Maintainer: Colin FAY <contact@colinfay.me>
Diff between languagelayeR versions 1.2.3 dated 2018-01-26 and 1.2.4 dated 2019-02-12
DESCRIPTION | 11 ++--- LICENSE | 2 - MD5 | 29 ++++++++------- NAMESPACE | 5 ++ NEWS.md |only R/get_lang.R | 79 +++++++++++++++++-------------------------- R/get_supported_lang.R | 68 ++++++++++++++++++------------------- R/utils.R | 46 ++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/Introduction.R | 2 - inst/doc/Introduction.Rmd | 4 +- inst/doc/Introduction.html | 26 ++++++-------- man/get_lang.Rd | 4 +- man/get_supported_lang.Rd | 4 +- tests/testthat/test_errors.R | 4 +- vignettes/Introduction.Rmd | 4 +- 16 files changed, 161 insertions(+), 127 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 0.7.1 dated 2019-01-21 and 0.7.2 dated 2019-02-12
DESCRIPTION | 17 ++++---- MD5 | 49 ++++++++++++++---------- NAMESPACE | 3 + NEWS.md | 8 +++ R/bandit4arm2_kalman_filter.R | 2 R/bandit4arm_2par_lapse.R |only R/bandit4arm_lapse_decay.R |only R/bandit4arm_singleA_lapse.R |only R/bart_par4.R | 2 R/dbdm_prob_weight.R | 1 R/hBayesDM.R | 53 ++++++++++++++------------ R/peer_ocu.R | 2 R/ts_par4.R | 2 R/ts_par6.R | 2 R/ts_par7.R | 2 inst/plotting/plot_functions.R | 31 +++++++++++++++ inst/stan_files/bandit4arm_2par_lapse.stan |only inst/stan_files/bandit4arm_lapse_decay.stan |only inst/stan_files/bandit4arm_singleA_lapse.stan |only man/bandit4arm2_kalman_filter.Rd | 6 +- man/bandit4arm_2par_lapse.Rd |only man/bandit4arm_lapse_decay.Rd |only man/bandit4arm_singleA_lapse.Rd |only man/bart_par4.Rd | 2 man/dbdm_prob_weight.Rd | 2 man/hBayesDM-package.Rd | 37 ++++++++++-------- man/peer_ocu.Rd | 2 man/ts_par4.Rd | 2 man/ts_par6.Rd | 2 man/ts_par7.Rd | 2 30 files changed, 149 insertions(+), 80 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5 dated 2019-01-10 and 1.5.1 dated 2019-02-12
DESCRIPTION | 8 +- MD5 | 172 +++++++++++++++++++++++++------------------------- R/Effectsize.R | 17 +++- man/ABWilcox.Rd | 4 - man/ABanova.Rd | 5 - man/ABarrow.Rd | 6 - man/ABautoacf.Rd | 4 - man/ABautopacf.Rd | 4 - man/ABbinomial.Rd | 4 - man/ABdescrip.Rd | 4 - man/ABiqr.Rd | 4 - man/ABlineD.Rd | 4 - man/ABlines.Rd | 4 - man/ABma.Rd | 4 - man/ABplot.Rd | 4 - man/ABplotm.Rd | 4 - man/ABregres.Rd | 4 - man/ABrf2.Rd | 4 - man/ABrobust.Rd | 4 - man/ABstat.Rd | 4 - man/ABtext.Rd | 4 - man/ABtsplot.Rd | 4 - man/ABttest.Rd | 4 - man/Append.Rd | 4 - man/Aregres.Rd | 4 - man/Arimadiff.Rd | 4 - man/Arimama.Rd | 4 - man/Arobust.Rd | 4 - man/Cchart.Rd | 4 - man/Effectsize.Rd | 4 - man/GABrf2.Rd | 4 - man/GABttest.Rd | 4 - man/Getcsv.Rd | 4 - man/Gindex.Rd | 5 - man/Gline.Rd | 4 - man/Gmedian.Rd | 4 - man/IQRbandgraph.Rd | 4 - man/IQRlegend.Rd | 4 - man/IQRline.Rd | 4 - man/PANDlegend.Rd | 4 - man/PEMabove.Rd | 4 - man/PEMbelow.Rd | 4 - man/PNDbelow.Rd | 4 - man/PNDlegend.Rd | 4 - man/Pchart.Rd | 4 - man/Rchart.Rd | 4 - man/Rchartsd.Rd | 5 - man/SD1.Rd | 5 - man/SD1legend.Rd | 4 - man/SD2.Rd | 4 - man/SD2legend.Rd | 4 - man/SDAband.Rd | 4 - man/SN.Rd | 4 - man/SPClegend.Rd | 5 - man/SPCline.Rd | 4 - man/SSDforR.Rd | 2 man/Savecsv.Rd | 4 - man/Trimline.Rd | 5 - man/XRchart.Rd | 4 - man/Xmrchart.Rd | 5 - man/cdcabove.rd | 5 - man/cdcbelow.rd | 5 - man/diffchart.Rd | 5 - man/insert.rd | 5 - man/ird.rd | 4 - man/listnames.rd | 5 - man/meanES.Rd | 5 - man/meanabove.rd | 4 - man/meanbelow.rd | 4 - man/medabove.rd | 4 - man/medbelow.rd | 4 - man/metareg.Rd | 4 - man/pandabove.rd | 4 - man/pandbelow.rd | 4 - man/pemlegend.rd | 4 - man/plotnum.Rd | 4 - man/pndabove.rd | 4 - man/regabove.Rd | 5 - man/regbelow.Rd | 4 - man/robregabove.Rd | 5 - man/robregbelow.Rd | 4 - man/robustCDCabove.Rd | 4 - man/robustCDCbelow.Rd | 4 - man/sd1bandgraph.rd | 4 - man/sd2bandgraph.rd | 4 - man/trimabove.Rd | 4 - man/trimbelow.Rd | 4 - 87 files changed, 119 insertions(+), 429 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.11.0 dated 2019-01-12 and 2.12.0 dated 2019-02-12
datarobot-2.11.0/datarobot/R/DeleteProject.R |only datarobot-2.11.0/datarobot/R/GetModelJobs.R |only datarobot-2.11.0/datarobot/R/GetProject.R |only datarobot-2.11.0/datarobot/R/GetProjectList.R |only datarobot-2.11.0/datarobot/R/GetProjectStatus.R |only datarobot-2.11.0/datarobot/R/UpdateProject.R |only datarobot-2.11.0/datarobot/inst/doc/ModelDeployments.R |only datarobot-2.11.0/datarobot/inst/doc/ModelDeployments.Rmd |only datarobot-2.11.0/datarobot/inst/doc/ModelDeployments.html |only datarobot-2.12.0/datarobot/DESCRIPTION | 10 datarobot-2.12.0/datarobot/MD5 | 134 +-- datarobot-2.12.0/datarobot/NAMESPACE | 7 datarobot-2.12.0/datarobot/NEWS | 24 datarobot-2.12.0/datarobot/R/ConnectToDataRobot.R | 2 datarobot-2.12.0/datarobot/R/ConnectionViewer.R | 6 datarobot-2.12.0/datarobot/R/DataRobotRequests.R | 65 + datarobot-2.12.0/datarobot/R/DeleteModelJob.R | 4 datarobot-2.12.0/datarobot/R/DeletePredictJob.R | 3 datarobot-2.12.0/datarobot/R/Features.R | 11 datarobot-2.12.0/datarobot/R/Jobs.R | 4 datarobot-2.12.0/datarobot/R/LiftChart.R | 13 datarobot-2.12.0/datarobot/R/ListModelJobs.R |only datarobot-2.12.0/datarobot/R/MissingValuesReport.R |only datarobot-2.12.0/datarobot/R/Models.R | 58 + datarobot-2.12.0/datarobot/R/PredictionDatasets.R | 37 + datarobot-2.12.0/datarobot/R/PrimeFiles.R | 2 datarobot-2.12.0/datarobot/R/PrimeModels.R | 2 datarobot-2.12.0/datarobot/R/Projects.R |only datarobot-2.12.0/datarobot/R/RocCurve.R | 21 datarobot-2.12.0/datarobot/R/StartAutopilot.R | 56 + datarobot-2.12.0/datarobot/R/WaitForAutopilot.R | 4 datarobot-2.12.0/datarobot/R/asDataFrame.R | 31 datarobot-2.12.0/datarobot/R/summaryMethods.R | 2 datarobot-2.12.0/datarobot/inst/doc/AdvancedVignette.R | 19 datarobot-2.12.0/datarobot/inst/doc/AdvancedVignette.Rmd | 33 datarobot-2.12.0/datarobot/inst/doc/AdvancedVignette.html | 41 - datarobot-2.12.0/datarobot/man/CreateDataSource.Rd | 3 datarobot-2.12.0/datarobot/man/CreateDatetimePartitionSpecification.Rd | 9 datarobot-2.12.0/datarobot/man/CreateUserPartition.Rd | 5 datarobot-2.12.0/datarobot/man/DeleteJob.Rd | 2 datarobot-2.12.0/datarobot/man/DeleteModelJob.Rd | 4 datarobot-2.12.0/datarobot/man/DeleteProject.Rd | 4 datarobot-2.12.0/datarobot/man/GetAllLiftCharts.Rd | 21 datarobot-2.12.0/datarobot/man/GetAllRocCurves.Rd | 29 datarobot-2.12.0/datarobot/man/GetDatetimeModelFromJobId.Rd | 2 datarobot-2.12.0/datarobot/man/GetFrozenModelFromJobId.Rd | 2 datarobot-2.12.0/datarobot/man/GetJob.Rd | 2 datarobot-2.12.0/datarobot/man/GetMissingValuesReport.Rd |only datarobot-2.12.0/datarobot/man/GetModelFromJobId.Rd | 2 datarobot-2.12.0/datarobot/man/GetModelJob.Rd | 4 datarobot-2.12.0/datarobot/man/GetModelJobs.Rd | 46 - datarobot-2.12.0/datarobot/man/GetPrimeFileFromJobId.Rd | 2 datarobot-2.12.0/datarobot/man/GetPrimeModelFromJobId.Rd | 2 datarobot-2.12.0/datarobot/man/GetProject.Rd | 4 datarobot-2.12.0/datarobot/man/GetProjectList.Rd | 56 - datarobot-2.12.0/datarobot/man/GetProjectStatus.Rd | 2 datarobot-2.12.0/datarobot/man/GetRatingTableModelFromJobId.Rd | 3 datarobot-2.12.0/datarobot/man/ListLiftCharts.Rd |only datarobot-2.12.0/datarobot/man/ListModelJobs.Rd |only datarobot-2.12.0/datarobot/man/ListModels.Rd | 2 datarobot-2.12.0/datarobot/man/ListProjects.Rd |only datarobot-2.12.0/datarobot/man/ListRocCurves.Rd |only datarobot-2.12.0/datarobot/man/MakeDataRobotRequest.Rd |only datarobot-2.12.0/datarobot/man/RequestNewModel.Rd | 13 datarobot-2.12.0/datarobot/man/RequestReasonCodes.Rd | 4 datarobot-2.12.0/datarobot/man/RequestSampleSizeUpdate.Rd | 3 datarobot-2.12.0/datarobot/man/SetTarget.Rd | 8 datarobot-2.12.0/datarobot/man/SetupProjectFromHDFS.Rd | 4 datarobot-2.12.0/datarobot/man/SetupProjectFromPostgreSQL.Rd | 4 datarobot-2.12.0/datarobot/man/StartProject.Rd |only datarobot-2.12.0/datarobot/man/UpdateDataSource.Rd | 6 datarobot-2.12.0/datarobot/man/UpdateProject.Rd | 2 datarobot-2.12.0/datarobot/man/UploadPredictionDataset.Rd | 3 datarobot-2.12.0/datarobot/man/UploadPredictionDatasetFromDataSource.Rd |only datarobot-2.12.0/datarobot/man/as.data.frame.Rd | 15 datarobot-2.12.0/datarobot/man/summary.dataRobotModel.Rd | 2 datarobot-2.12.0/datarobot/tests/testthat/test-StartAutopilot.R | 360 +++++++--- datarobot-2.12.0/datarobot/vignettes/AdvancedVignette.Rmd | 33 78 files changed, 783 insertions(+), 469 deletions(-)
Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection
Analysis
Description: Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions
that help to create regression models for some genomic models proposed by Montesinos-López, et al. (2016) <doi:10.1534/g3.116.032359>
also in Montesinos-López et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-López et al. (2018) <doi:10.2134/agronj2018.06.0362>.
Author: Francisco Javier Luna-Vazquez [aut, cre]
(<https://orcid.org/0000-0002-5370-7152>),
Fernando H. Toledo [aut],
Osval Antonio Montesinos-Lopez [aut]
(<https://orcid.org/0000-0002-3973-6547>),
Abelardo Montesinos-Lopez [aut],
Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Diff between BMTME versions 1.0.5 dated 2019-02-02 and 1.0.6 dated 2019-02-12
DESCRIPTION | 10 ++-- MD5 | 20 ++++----- NEWS.md | 7 +++ R/BME.R | 5 +- R/BMTME.R | 5 +- R/cholesky.R | 1 inst/doc/bme.html | 101 ++++++++++++++++++++++--------------------------- inst/doc/bmors.html | 6 +- inst/doc/bmorsenv.html | 6 +- inst/doc/bmtme.html | 58 ++++++++++++++-------------- tests/testthat/test.R | 71 +++++++++++++++++++--------------- 11 files changed, 151 insertions(+), 139 deletions(-)
Title: Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices
Description: Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.
Author: Daniel Fischer [aut, cre],
Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between hoardeR versions 0.9.4 dated 2019-02-07 and 0.9.4-2 dated 2019-02-12
hoardeR-0.9.4-2/hoardeR/DESCRIPTION | 8 +- hoardeR-0.9.4-2/hoardeR/MD5 | 16 ++-- hoardeR-0.9.4-2/hoardeR/inst/ChangeLog | 7 +- hoardeR-0.9.4-2/hoardeR/inst/doc/hoardeR-vignette.R | 2 hoardeR-0.9.4-2/hoardeR/inst/doc/hoardeR-vignette.Rmd | 2 hoardeR-0.9.4-2/hoardeR/inst/doc/hoardeR-vignette.pdf | 55 +++++++---------- hoardeR-0.9.4-2/hoardeR/man/hoardeR-package.Rd | 4 - hoardeR-0.9.4-2/hoardeR/vignettes/coverageExample.png |only hoardeR-0.9.4-2/hoardeR/vignettes/hoardeR-vignette.Rmd | 2 hoardeR-0.9.4/hoardeR/vignettes/coverageExample.jpg |only 10 files changed, 48 insertions(+), 48 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.13 dated 2018-08-17 and 1.0.14 dated 2019-02-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/pubtator_function.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (Theoretical Ecology, University of
Regensburg, Regensburg, Germany)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.2.2 dated 2019-01-20 and 0.2.3 dated 2019-02-12
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 7 +++++++ R/DHARMa.R | 5 ++++- R/compatibility.R | 18 ++++++++++++++++++ R/plotResiduals.R | 2 +- R/simulateResiduals.R | 29 ++++++++--------------------- inst/doc/DHARMa.Rmd | 3 ++- inst/doc/DHARMa.html | 27 ++++----------------------- man/DHARMa.Rd | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/testModelTypes.R | 2 +- vignettes/DHARMa.Rmd | 3 ++- 13 files changed, 64 insertions(+), 66 deletions(-)